Zen Shiatsu and the 5 Element points...Help!

This can get a little elaborate (like most things in TCM), but I think this will help. Generally speaking when you use acupuncture points you can tonify the meridian by needling with the flow of the meridian and disperse the meridian by needling against the flow of the meridian. In general this theory is to effect the excess/deficiency patterns in a particular meridian. So excess energy in the face (sinus, etc.) you can disperse LU 7. Weakness in the lungs (deficiency asthma, etc.) you can tonify LU 9. Note that these points also individually have dispersive and tonification actions separately from simply the direction of flow. Thus, the directions of needling/flow of the meridians is somewhat (generally, again) outside of the function of each individual point.

Entry/Exit point needling is a somewhat separate theory. For details on this theory you can read the entry/exit details section. And for a general statement that will take away some of your concerns about this apparent contradiction in function at times, I state on that page "The entry exit points do not have a strong theoretical usage in modern clinical practice, however, they may be considered if you want to allow a relative excess or deficiency in one meridian to be offset by it's yin yang paired meridian." (Again a somewhat generalized statement, but clinically valid for most practitioners)

You might also want to read the entry exit block theory from classical five element treatment section. Five Element Acupuncture and TCM style Acupuncture often use these theories in different ways or place higher levels of emphasis on certain theories and less on others.